Input and runtime details for job 5172788 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
73	0.002141	0.09621	b0740	tolB	-11.17	0.098836	117 -- 150	8 -- 46	periplasmic protein	_____________116______________________________________151\n_____________\|________________________________________\|\n5'-UCC...GCCAC______________GUUUUGU___________________AACAU...CCG-3'\n______________GG_GGUU_CUGGUA_______GUAUUUUA___GUU_UGUU\n______________\|\|_\|\|\|\|_\|\|\|\|\|\|_______\|:\|\|\|\|\|\|___\|\|\|_\|\|\|\|\n______________CC_CCAA_GACCAU_______CGUAAAAU___CAA_ACAA\n3'-UUU...UUCCU__A____G______GUCGAU_________ACC___U____AAAGUCG-5'\n_____________\|________________________________________\|\n_____________47_______________________________________7\n	137 -- 143	19 -- 25	-23.6895 kcal/mol	7.90884 kcal/mol	4.60831 kcal/mol	116 151@LB@ \| \|@LB@5'-UCC...GCCAC GUUUUGU AACAU...CCG-3'@LB@ GG GGUU CUGGUA GUAUUUUA GUU UGUU@LB@ \|\| \|\|\|\| \|\|\|\|\|\| \|:\|\|\|\|\|\| \|\|\| \|\|\|\|@LB@ CC CCAA GACCAU CGUAAAAU CAA ACAA@LB@3'-UUU...UUCCU A G GUCGAU ACC U AAAGUCG-5'@LB@ \| \|@LB@ 47 7@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -23.6895 kcal/mol@LB@Unfolding Energy - mRNA 7.90884 kcal/mol@LB@Unfolding Energy - sRNA 4.60831 kcal/mol@LB@@LB@Position - mRNA 117 -- 150@LB@Position - sRNA 8 -- 46@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 19 -- 25@LB@
164	0.008548	0.1748	b0461	tomB	-9.85	0.177976	15 -- 39	9 -- 30	Hha toxicity attenuator; conjugation-related protein	_____________14________________________40\n_____________\|_________________________\|\n5'-UGC...UUAGU________GAAAAA___A__CC___CCCGC...AUC-3'\n______________GCUAGUAU______GUG_GU__UGU\n______________\|\|\|\|\|:\|\|______:\|\|_\|\|__\|\|\|\n______________CGAUCGUA______UAC_CA__ACA\n3'-UUU...CAUGU________AAA______C__AU___AAAAGUCG-5'\n_____________\|_________________________\|\n_____________31________________________8\n	16 -- 22	23 -- 29	-13.2091 kcal/mol	1.89111 kcal/mol	1.4702 kcal/mol	14 40@LB@ \| \|@LB@5'-UGC...UUAGU GAAAAA A CC CCCGC...AUC-3'@LB@ GCUAGUAU GUG GU UGU@LB@ \|\|\|\|\|:\|\| :\|\| \|\| \|\|\|@LB@ CGAUCGUA UAC CA ACA@LB@3'-UUU...CAUGU AAA C AU AAAAGUCG-5'@LB@ \| \|@LB@ 31 8@LB@@LB@@LB@Energy -9.85 kcal/mol@LB@Hybridization Energy -13.2091 kcal/mol@LB@Unfolding Energy - mRNA 1.89111 kcal/mol@LB@Unfolding Energy - sRNA 1.4702 kcal/mol@LB@@LB@Position - mRNA 15 -- 39@LB@Position - sRNA 9 -- 30@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 23 -- 29@LB@
189	0.01085	0.1919	b3606	trmL	-8.64	0.283903	120 -- 126	63 -- 69	tRNA Leu mC34 mU34 2'-O-methyltransferase SAM-dependent	_____________119_____127\n_____________\|_______\|\n5'-UAG...CCUCC_______GGGCC...AAC-3'\n______________GGGGAGA\n______________:\|\|\|\|\|\|\n______________UCCCUCU\n3'-UUU...CACAU_______AAUGU...UCG-5'\n_____________\|_______\|\n_____________70______62\n	120 -- 126	63 -- 69	-10.8913 kcal/mol	1.31422 kcal/mol	0.939295 kcal/mol	119 127@LB@ \| \|@LB@5'-UAG...CCUCC GGGCC...AAC-3'@LB@ GGGGAGA@LB@ :\|\|\|\|\|\|@LB@ UCCCUCU@LB@3'-UUU...CACAU AAUGU...UCG-5'@LB@ \| \|@LB@ 70 62@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -10.8913 kcal/mol@LB@Unfolding Energy - mRNA 1.31422 kcal/mol@LB@Unfolding Energy - sRNA 0.939295 kcal/mol@LB@@LB@Position - mRNA 120 -- 126@LB@Position - sRNA 63 -- 69@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 63 -- 69@LB@
44	0.0009392	0.07174	b3453	ugpB	-12.21	0.059079	239 -- 268	1 -- 32	sn-glycerol-3-phosphate ABC transporter periplasmic binding protein	_____________238_______________________________269\n_____________\|_________________________________\|\n5'-UUC...GCGCU___A________A______GA___CACA_____AGUGA...UGG-3'\n______________CGG_CUGGCGUU__AUGGG__AUG______GGC\n______________\|:\|_\|\|:\|\|:\|\|__\|\|\|\|\|__\|\|\|______:\|\|\n______________GUC_GAUCGUAA__UACCC__UAC______UCG\n3'-UUU...ACCAU____________AA_____AA___AAAAAG___-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	244 -- 250	22 -- 28	-24.6308 kcal/mol	10.9347 kcal/mol	1.49075 kcal/mol	238 269@LB@ \| \|@LB@5'-UUC...GCGCU A A GA CACA AGUGA...UGG-3'@LB@ CGG CUGGCGUU AUGGG AUG GGC@LB@ \|:\| \|\|:\|\|:\|\| \|\|\|\|\| \|\|\| :\|\|@LB@ GUC GAUCGUAA UACCC UAC UCG@LB@3'-UUU...ACCAU AA AA AAAAAG -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.21 kcal/mol@LB@Hybridization Energy -24.6308 kcal/mol@LB@Unfolding Energy - mRNA 10.9347 kcal/mol@LB@Unfolding Energy - sRNA 1.49075 kcal/mol@LB@@LB@Position - mRNA 239 -- 268@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 22 -- 28@LB@
173	0.009278	0.1803	b3495	uspA	-10.68	0.124344	253 -- 279	16 -- 40	universal stress global response regulator	_____________252_________________________280\n_____________\|___________________________\|\n5'-GUC...CAAAG________G__AA____GUCUC_____CUCGC...AAG-3'\n______________UUCUGGUA_AG__AGCA_____UAUGG\n______________\|:\|\|\|\|\|\|_\|\|__\|\|\|\|_____\|\|\|\|\|\n______________AGGACCAU_UC__UCGU_____AUACC\n3'-UUU...CACCA________G__GA____AAA_______CAAUA...UCG-5'\n_____________\|___________________________\|\n_____________41__________________________15\n	254 -- 260	33 -- 39	-24.2729 kcal/mol	9.02768 kcal/mol	4.56874 kcal/mol	252 280@LB@ \| \|@LB@5'-GUC...CAAAG G AA GUCUC CUCGC...AAG-3'@LB@ UUCUGGUA AG AGCA UAUGG@LB@ \|:\|\|\|\|\|\| \|\| \|\|\|\| \|\|\|\|\|@LB@ AGGACCAU UC UCGU AUACC@LB@3'-UUU...CACCA G GA AAA CAAUA...UCG-5'@LB@ \| \|@LB@ 41 15@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -24.2729 kcal/mol@LB@Unfolding Energy - mRNA 9.02768 kcal/mol@LB@Unfolding Energy - sRNA 4.56874 kcal/mol@LB@@LB@Position - mRNA 253 -- 279@LB@Position - sRNA 16 -- 40@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 33 -- 39@LB@
149	0.00724	0.1633	b3494	uspB	-9.24	0.227320	190 -- 228	15 -- 51	universal stress (ethanol tolerance) protein B	_____________189_____________________________________229\n_____________\|_______________________________________\|\n5'-AAU...UCGCC_______A___AUGAUAA___C_GUC_____AUUU____CUUUA...UGC-3'\n______________GGGGAGG_GGU_______GCA_C___GCAUU____UGGG\n______________::\|\|\|\|\|_\|\|\|_______:\|\|_\|___\|\|\|\|\|____\|\|\|\|\n______________UUCCUCC_CCA_______UGU_G___CGUAA____ACCC\n3'-UUU...UCCGA_______A___AGGACCA___C_AU______AAU_____AAUAC...UCG-5'\n_____________\|_______________________________________\|\n_____________52______________________________________14\n	190 -- 196	45 -- 51	-24.8188 kcal/mol	10.9257 kcal/mol	4.65724 kcal/mol	189 229@LB@ \| \|@LB@5'-AAU...UCGCC A AUGAUAA C GUC AUUU CUUUA...UGC-3'@LB@ GGGGAGG GGU GCA C GCAUU UGGG@LB@ ::\|\|\|\|\| \|\|\| :\|\| \| \|\|\|\|\| \|\|\|\|@LB@ UUCCUCC CCA UGU G CGUAA ACCC@LB@3'-UUU...UCCGA A AGGACCA C AU AAU AAUAC...UCG-5'@LB@ \| \|@LB@ 52 14@LB@@LB@@LB@Energy -9.24 kcal/mol@LB@Hybridization Energy -24.8188 kcal/mol@LB@Unfolding Energy - mRNA 10.9257 kcal/mol@LB@Unfolding Energy - sRNA 4.65724 kcal/mol@LB@@LB@Position - mRNA 190 -- 228@LB@Position - sRNA 15 -- 51@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 45 -- 51@LB@
20	0.0001678	0.0282	b2056	wcaD	-17.66	0.001373	77 -- 104	24 -- 48	putative colanic acid polymerase	_____________76___________________________105\n_____________\|____________________________\|\n5'-GCC...AAGAA______CUGCAA____________A___AACCG...UCA-3'\n______________GAGGUG______CUGGUGCAGUUA_GCA\n______________\|\|\|\|\|\|______\|\|\|\|\|:\|\|\|:\|\|_\|\|\|\n______________CUCCAC______GACCAUGUCGAU_CGU\n3'-UUU...GAUUC______CAAG__________________AAAAU...UCG-5'\n_____________\|____________________________\|\n_____________49___________________________23\n	94 -- 100	27 -- 33	-32.1729 kcal/mol	9.95006 kcal/mol	4.55899 kcal/mol	76 105@LB@ \| \|@LB@5'-GCC...AAGAA CUGCAA A AACCG...UCA-3'@LB@ GAGGUG CUGGUGCAGUUA GCA@LB@ \|\|\|\|\|\| \|\|\|\|\|:\|\|\|:\|\| \|\|\|@LB@ CUCCAC GACCAUGUCGAU CGU@LB@3'-UUU...GAUUC CAAG AAAAU...UCG-5'@LB@ \| \|@LB@ 49 23@LB@@LB@@LB@Energy -17.66 kcal/mol@LB@Hybridization Energy -32.1729 kcal/mol@LB@Unfolding Energy - mRNA 9.95006 kcal/mol@LB@Unfolding Energy - sRNA 4.55899 kcal/mol@LB@@LB@Position - mRNA 77 -- 104@LB@Position - sRNA 24 -- 48@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 27 -- 33@LB@
71	0.001933	0.09081	b2044	wcaL	-10.40	0.140507	12 -- 21	24 -- 33	putative glycosyl transferase	_____________11_________22\n_____________\|__________\|\n5'-GGG...AUGCA________G_CUACC...AGA-3'\n______________GCAGCUGG_A\n______________:\|\|\|\|\|:\|_\|\n______________UGUCGAUC_U\n3'-UUU...GACCA________G_AAAAU...UCG-5'\n_____________\|__________\|\n_____________34_________23\n	13 -- 19	26 -- 32	-13.1871 kcal/mol	1.35791 kcal/mol	1.42716 kcal/mol	11 22@LB@ \| \|@LB@5'-GGG...AUGCA G CUACC...AGA-3'@LB@ GCAGCUGG A@LB@ :\|\|\|\|\|:\| \|@LB@ UGUCGAUC U@LB@3'-UUU...GACCA G AAAAU...UCG-5'@LB@ \| \|@LB@ 34 23@LB@@LB@@LB@Energy -10.40 kcal/mol@LB@Hybridization Energy -13.1871 kcal/mol@LB@Unfolding Energy - mRNA 1.35791 kcal/mol@LB@Unfolding Energy - sRNA 1.42716 kcal/mol@LB@@LB@Position - mRNA 12 -- 21@LB@Position - sRNA 24 -- 33@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 26 -- 32@LB@
134	0.005847	0.146	b0065	yabI	-9.48	0.206647	266 -- 290	24 -- 46	DedA family inner membrane protein	_____________265_______________________291\n_____________\|_________________________\|\n5'-UGA...GUGUU_____CC_______AGUC_______CUGGU...GUU-3'\n______________GGUGG__UUUCUGG____GCUGGCG\n______________\|\|\|\|\|__\|\|:\|\|\|\|____\|\|\|:\|\|:\n______________CCACC__AAGGACC____CGAUCGU\n3'-UUU...UUCCU______________AUGU_______AAAAU...UCG-5'\n_____________\|_________________________\|\n_____________47________________________23\n	284 -- 290	24 -- 30	-26.6068 kcal/mol	12.5692 kcal/mol	4.55813 kcal/mol	265 291@LB@ \| \|@LB@5'-UGA...GUGUU CC AGUC CUGGU...GUU-3'@LB@ GGUGG UUUCUGG GCUGGCG@LB@ \|\|\|\|\| \|\|:\|\|\|\| \|\|\|:\|\|:@LB@ CCACC AAGGACC CGAUCGU@LB@3'-UUU...UUCCU AUGU AAAAU...UCG-5'@LB@ \| \|@LB@ 47 23@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -26.6068 kcal/mol@LB@Unfolding Energy - mRNA 12.5692 kcal/mol@LB@Unfolding Energy - sRNA 4.55813 kcal/mol@LB@@LB@Position - mRNA 266 -- 290@LB@Position - sRNA 24 -- 46@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 24 -- 30@LB@
47	0.001093	0.07744	b0128	yadH	-6.67	0.521304	272 -- 286	25 -- 36	putative ABC transporter permease	_____________271_____________287\n_____________\|_______________\|\n5'-UUA...AUCUG_______ACG_____GCCGC...UCA-3'\n______________GGUGCAG___CUGGU\n______________\|\|\|:\|\|\|___\|\|:\|:\n______________CCAUGUC___GAUCG\n3'-UUU...AAGGA_______________UAAAA...UCG-5'\n_____________\|_______________\|\n_____________37______________24\n	272 -- 278	30 -- 36	-13.5693 kcal/mol	5.47586 kcal/mol	1.42738 kcal/mol	271 287@LB@ \| \|@LB@5'-UUA...AUCUG ACG GCCGC...UCA-3'@LB@ GGUGCAG CUGGU@LB@ \|\|\|:\|\|\| \|\|:\|:@LB@ CCAUGUC GAUCG@LB@3'-UUU...AAGGA UAAAA...UCG-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -6.67 kcal/mol@LB@Hybridization Energy -13.5693 kcal/mol@LB@Unfolding Energy - mRNA 5.47586 kcal/mol@LB@Unfolding Energy - sRNA 1.42738 kcal/mol@LB@@LB@Position - mRNA 272 -- 286@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 30 -- 36@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

service.

When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching